*************************************************************************
Changes in version 0.20.6
*************************************************************************
FIXES
o fixed new NOTEs in R CMD check (about requireNamespace)
o fixed error in heatmaps due to new version of stringr (>= 1.0.0)
*************************************************************************
Changes in version 0.20
*************************************************************************
NEW FEATURES
o aheatmap gains an argument txt that enables displaying text in each
cell of the heatmap.
FIXES
o now all examples, vignettes and unit tests comply with CRAN policies
on the maximum number of cores to be used when checking packages (2).
*************************************************************************
Changes in version 0.18
*************************************************************************
NEW FEATURES
o aheatmap gains distfun methods 'spearman', 'kendall', and,
for completeness, 'pearson' (for which 'correlation' is now an alias),
which specifies the correlation method to use when computing the
distance matrix.
CHANGES
o In order to fully comply with CRAN policies, internals of the
aheatmap function slightly changed. In particular, this brings an
issue when directly plotting to PDF graphic devices, where a first
blank page may appear. See the dedicated section in the man page
?aheatmap for a work around.
*************************************************************************
Changes in version 0.17.3
*************************************************************************
NEW FEATURES
o add silhouette computation for NMF results, which can be performed on
samples, features or consensus matrix.
The average silhouette width is also computed by the summary methods.
(Thanks to Gordon Robertson for this suggestion)
o New runtime option 'shared.memory' (or 'm') for toggling usage of shared
memory (requires package synchronicity).
CHANGES
o some plots are -- finally -- generated using ggplot2
This adds an Imports dependency to ggplot2 and reshape2.
BUG FIXES
o fix a bug when running parallel NMF computation with
algorithms defined in other packages (this most probably only affected my
own packages, e.g., CellMix)
*************************************************************************
Changes in version 0.17.1
*************************************************************************
CHANGES
o Computations seeded with an NMF object now set slot @seed to 'NMF'
o Added unit tests on seeding with an NMF object
o Removed some obsolete comments
BUG FIXES
o an error was thrown when running multiple sequential NMF
computations with nrun>=50: object '.MODE_SEQ' not found.
(reported by Kenneth Lopiano)
*************************************************************************
Changes in version 0.16.5
*************************************************************************
CHANGES
o Now depends on pkgmaker 0.16
o Disabled shared memory on Mac machines by default, due to un-resolved
bug that occurs with big-matrix descriptors.
It can be restored using nmf.options(shared.memory=TRUE)
o Package version is now shown on startup message
o Re-enabled unit test checks on CRAN, using the new function
pkgmaker::isCHECK, that definitely identifies if tests are run
under R CMD check.
*************************************************************************
* Changes in version 0.15.2 *
*************************************************************************
NEW FEATURES
o New function nmfObject() to update old versions of NMF objects,
eg., saved on disk.
o NMF strategies can now define default values for their parameters,
eg., `seed` to associate them with a seeding method that is not the
default method, `maxIter` to make default runs with more iterations
(for algorithms defined as NMFStrategyIterative), or any other
algorithm-specific parameter.
o new general utility function hasArg2 that is identical to hasArg
but takes the argument name as a character string, so that no
check NOTE is thrown.
CHANGES
o All vignettes are now generated using knitr.
o New dependency to pkgmaker which incorporated many of the
general utility functions, initially defined for the NMF package.
o example check is faster (as requested by CRAN)
o the function selectMethodNMF was renamed into selectNMFMethod to
be consistent with the other related *NMFMethod functions (get, set, etc..)
FIXES
o Fix computation of R-squared in profplot/corplot: now compute from
a linear fit that includes an intercept.
*************************************************************************
* Changes in version 0.8.6 *
*************************************************************************
NEW FEATURES
o Formula based NMF models that can incorporate fixed terms, which may
be used to correct for covariates or define group specific offsets.
CHANGES
o Subsetting an NMF object with a single index now returns an NMF object,
except if argument drop is not missing (i.e. either TRUE or FALSE).
*************************************************************************
* Changes in version 0.6.03 *
*************************************************************************
WARNING
Due to the major changes made in the internal structure of the standard NMF
models, previous NMF fits are not compatible with this version.
NEW FEATURES
o The factory function nmfModel has been enhanced and provides new
methods that makes more easier the creation of NMF objects.
See ?nmfModel.
o A new heatmap drawing function 'aheatmap' (for annotated heatmap) is
now used to generate the different heatmaps (basismap, coefmap and consensusmap).
It is a enhancement/fork of the function pheatmap from package pheatmap and draw
-- I think -- very nice heatmaps, providing a convenient and flexible
interface to add annotation tracks to both the columns and rows, with
sensible automatic legends.
CHANGES
o Method nmfModel when called with no arguments does not return anymore
the list of available NMF models, but an empty NMF model.
To list the available models, directly call `nmfModels()`.
o The function `rmatrix` is now a S4 generic function.
It gains methods for generating random matrices based on a template matrix
or an NMF model.
See ?rmatrix.
o The function `rnmf` gains a method to generate a random NMF model
given numerical dimensions.
o The function nmfEstimateRank now returns the fits for each value of the
rank in element 'fit' of the result list.
See ?nmfEstimateRank.
*************************************************************************
* Changes in version 0.5.3 *
*************************************************************************
NEW FEATURES
o The state of the random number generator is systematically stored in the
'NMFfit' object returned by function 'nmf'.
It is stored in a new slot 'rng.seed' and can be access via the new method
'rngSeed' of class 'NMFfit'.
See ?rngSeed for more details.
o The number of cores to use in multicore computations can now also be
specified by the 'p - parallel' runtime option (e.g. 'p4' to use 4 cores).
Note that the value specified in option 'p' takes precedence on the one
passed via argument '.pbackend'.
See section 'Runtime options' in ?nmf for more details.
o Function 'nmfApply' now allows values 3 and 4 for argument 'MARGIN' to
apply a given function to the basis vectors (i.e. columns of the basis matrix W)
and basis profiles (i.e. rows of the mixture coefficients H) respectively.
See ?nmfApply for more details.
o New S4 generic 'basiscor' and 'profcor' to compute the
correlation matrices of the basis vectors and basis profiles respectively
from two NMF models or from an NMF model and a given compatible matrix.
See ?basiscor or ?profcor for more details.
o New S4 generic 'fitcmp' to compare the NMF models fitted by two
different runs of function 'nmf' (i.e. two 'NMFfit' objects).
See ?fitcmp for more details.
o New S4 generic 'canFit' that tells if an NMF method is able to
exactly or partly fit a given NMF model.
See ?canFit for more details.
o New function 'selectMethodNMF' that selects an appropriate NMF method to
fit a given NMF model.
See ?selectMethodNMF for more details.
o The verbosity level can be controlled more finely by the 'v - verbose'
runtime option (e.g. using .options='v1' or 'v2'). The greater is
the level the more information is printed.
The verbose outputs have been cleaned-up and should be more consistent
across the run mode (sequential or multicore).
See section 'Runtime options' in ?nmf for more details.
CHANGES
o The standard update equations have been optimised further, by making
them modify the factor matrices in place. This speeds up the computation
and greatly improves the algorithms' memory footprint.
o The package NMF now depends on the package digest that is used to display
the state of random number generator in a concise way.
o The methods 'metaHeatmap' are split into 3 new S4 generic 'basismap' to
plot a heatmap of the basis matrix [formerly plotted by the call :
'metaHeatmap(object.of.class.NMF, 'features', ...) ], 'coefmap' to plot a
heatmap of the mixture coefficient matrix [formerly plotted by the call :
'metaHeatmap(object.of.class.NMF, 'samples', ...) ], and 'consensusmap' to
plot a heatmap of the consensus matrix associated with multiple runs of NMF
[formerly plotted by the call : 'metaHeatmap(object.of.class.NMFfitX, ...) ].
BUG FIX
o In factory method 'nmfModel': the colnames (resp. rownames) of
matrix W (resp. H) are now correctly set when the rownames of H
(resp. the colnames of W) are not null.
NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Deprecated Generics/Methods
1) 'metaHeatmap,NMF' and 'metaHeatmap,NMFfitX' - S4 methods remain
with .Deprecated message.
They are replaced by the definition of 3 new S4 generic 'basismap',
'coefmap' and 'consensusmap'. See the related point in section
CHANGES above.
They will be completely removed from the package in the next version.
*************************************************************************
* Changes in version 0.5.1 *
*************************************************************************
BUG FIX
o fix a small bug in method 'rss' to allow argument 'target' to be a
'data.frame'. This was generating errors when computing the summary
measures and especially when the function 'nmfEstimateRank' was called
on a 'data.frame'. Thanks to Pavel Goldstein for reporting this.
*************************************************************************
* Changes in version 0.5 *
*************************************************************************
NEW FEATURES
o Method 'fcnnls' provides a user-friendly interface for the internal
function '.fcnnls' to solve non-nengative linear least square problems,
using the fast combinatorial approach from Benthem and Keenan (2004).
See '?fcnnls' for more details.
o New argument 'callback' in method 'nmf' allows to provide a callback
function when running multiple runs in default mode, that only keeps the
best result. The callback function is applied to the result of each run
before it possibly gets discarding. The results are stored in the
miscellaneous slot '.callback' accessible via the '$' operator (e.g. res$.callback).
See '?nmf' for more details.
o New method 'niter' to retrieve the number of iterations performed to fit
a NMF model. It is defined on objects of class 'NMFfit'.
o New function 'isNMFfit' to check if an object is a result from NMF fitting.
o New function 'rmatrix' to easily generate random matrices, and allow to specify the
distribution from which the entries are drawn. For example:
* 'rmatrix(100, 10)' generates a 100x10 matrix whose entries are drawn
from the uniform distribution
* 'rmatrix(100, 10, rnorm)' generates a 100x10 matrix whose entries are drawn
from the standard Normal distribution.
o New methods 'basisnames' and 'basisnames=4.x)
DO NEED to install the synchronicity package to be able to run multicore NMF
computations.
Versions of bigmemory prior to 4.x include the mutex functionality.
o Minor enhancement in error messages
o Method 'nmfModel' can now be called with arguments 'rank' and 'target'
swapped. This is for convenience and ease of use.
BUG FIX
o Argument 'RowSideColors' of the 'metaHeatmap' function is now correctly
subset according to the value of argument 'filter'. However the argument
must be named with its complete name 'RowSideColors', not assuming
partial match. See KNOWN ISSUES.
KNOWN ISSUES
o In the 'metaHeatmap' function, when argument 'filter' is not 'FALSE':
arguments 'RowSideColors', 'labRow', 'Rowv' that are intended to the
'heatmap.plus'-like function (and are used to label the rows) should be
named using their complete name (i.e. not assuming partial match),
otherwise the filtering is not applied to these argument and an error
is generated.
This issue will be fixed in a future release.
*************************************************************************
* Changes in version 0.4.3 *
*************************************************************************
CHANGES
o function 'nmfEstimateRank' has been enhanced:
-run options can be passed to each internal call to the 'nmf' function.
See ?nmfEstiamteRank and ?nmf for details on the supported options.
- a new argument 'stop' allows to run the estimation with fault tolerance,
skipping runs that throw an error. Summary measures for these runs are set
to NAs and a warning is thrown with details about the errors.
o in function 'plot.NMF.rank': a new argument 'na.rm' allows to remove from
the plots the ranks for which the measures are NAs (due to errors during the
estimation process with 'nmfEstimateRank').
BUG FIX
o Method 'consensus' is now exported in the NAMESPACE file.
Thanks to Gang Su for reporting this.
o Warnings and messages about loading packages are now suppressed.
This was particularly confusing for users that do not have the packages
and/or platform required for parallel computation: warnings were printed
whereas the computation was -- sequentially -- performed without
problem.
Thanks to Joe Maisog for reporting this.
*************************************************************************
* Changes in version 0.4.1 *
*************************************************************************
BUG FIX
o The 'metaHeatmap' function was not correctly handling row labels
when argument filter was not FALSE. All usual row formating in heatmaps
(label and ordering) are now working as expected.
Thanks to Andreas Schlicker, from The Netherlands Cancer Institute for
reporting this.
o An error was thrown on some environments/platforms (e.g. Solaris)
where not all the packages required for parallel computation were not
available -- even when using option 'p' ('p' in lower case), which
should have switched the computation to sequential.
This is solved and the error is only thrown when running NMF with
option 'P' (capital 'P').
o Not all the options were passed (e.g. 't' for tracking) in sequential
mode (option '-p').
o verbose/debug global nmf.options were not restored if a numerical random
seed were used.
CHANGES
o The 'metaHeatmap' function nows support passing the name of a filtering
method in argument 'filter', which is passed to method 'extractFeatures'.
See ?metaHeatmap.
o Verbose and debug messages are better handled. When running a parallel
computation of multiple runs, verbose messages from each run are shown only
in debug mode.
*************************************************************************
* Changes in version 0.4 *
*************************************************************************
NEW FEATURES
o Part of the code has been optimised in C++ for speed and memory efficiency:
- the multiplicative updates for reducing the KL divergence and the euclidean
distance have been optimised in C++. This significantly reduces the
computation time of the methods that make use of them: 'lee', 'brunet',
'offset', 'nsNMF' and 'lnmf'.
Old R version of the algorithm are still accessible with the suffix '.R#'.
- the computation of euclidean distance and KL divergence are implemented
in C++, and do not require the duplication of the original matrices as done
in R.
o Generic 'dimnames' is now defined for objects of class 'NMF' and returns
a list with 3 elements: the row names of the basis matrix, the column names
of the mixture coefficient matrix , and the column names of the basis matrix.
This implies that methods 'rownames' and 'columnames' are also available for
'NMF' objects.
o A new class structure has been developed to handle the results of multiple
NMF runs in a cleaner and more structured way:
- Class 'NMFfitX' defines a common interface for multiple NMF runs of a
single algorithm.
- Class 'NMFfitX1' handles the sub-case where only the best fit is returned.
In particular, this class allows to handle such results as if coming
from a single run.
- Class 'NMFfitXn' handles the sub-case where the list of all the fits
is returned.
- Class 'NMFList' handles the case of heterogeneous NMF runs (different
algorithms, different factorization rank, different dimension, etc...)
o The vignette contains more examples and details about the use of package.
o The package is compatible with both versions 3.x and 4.x of the bigmemory
package. This package is used when running multicore parallel computations.
With version 4.x of bigmemory, the synchronicity package is also required as
it provides the mutex functionality that used to be provided by bigmemory 3.x.
BUG FIX
o Running in multicore mode from the GUI on MacOS X is not allowed anymore as
it is not safe and were throwing an error ['The process has forked and ...'].
Thanks to Stephen Henderson from the UCL Cancer Institute (UK) for reporting this.
o Function 'nmf' now restores the random seed to its original value as before its call
with a numeric seed. This behaviour can be disabled with option 'restore.seed=FALSE' or '-r'
NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS
o Deprecated Generics/Methods
1) 'errorPlot' - S4 generic/methods remains with .Deprecated message.
It is replaced by a definition of the 'plot' method for signatures
'NMFfit,missing' and 'NMFList,missing'
It will be completely removed from the package in the next version.
o Deprecated Class
1) 'NMFSet' - S4 class remains for backward compatibility, but is not
used anymore. It is replaced by the classes 'NMFfitX1', 'NMFfitXn',
'NMFList'.
*************************************************************************
* Changes in version 0.3 *
*************************************************************************
NEW FEATURES
o Now requires R 2.10
o New list slot 'misc' in class 'NMF' to be able to define new NMF models,
without having to extend the S4 class. Access is done by methods '$' and '$